How To Make Two Objects into One Mesh and then Only Animate One Object (Rotation)
I'm going to say that your importer or exporter is defective.  I am also not optimistic that unifying the mesh will solve things since it actually complicates things.

If you want to have a single mesh where part of it is animated, the first thing that comes to my mind is an armature paired with vertex groups.

You will need to assign all the vertices of the moving part of the mesh to a vertex group.  Select the mesh.  Enter edit mode.  Select the vertices for the animated part.  In the Mesh/ObjectData panel use the Vertex Group subpanel + button to create a new vertex group.  Then use the Assign button to add all those vertices to the group.  Double check that the weight is 1.0 (sometimes it is 0.0, which is almost useless).

Go back to Object mode and add a new Armature.  By default its single bone will be named "Bone".  Switch to edit mode, select the bone, and go to the Bone/ObjectData panel and rename it to match the vertex group of the mesh (which is probably named "Group").

Go back to Object mode.  Select the mesh.  Go to the Modifiers panel and add an Armature modifier (under the Deform section).  Choose the Armature as the modifier's object.  Make sure the Vertex Groups is checked.

Now you can select the armature and go into Pose mode (usually Ctrl-Tab) and put some keyframes on the bone to animate it rotating.  

Because the bone and the vertex groups have matching names, the armature modifier will make the object deform according to the motions of the bone.

As you can see, this rig is much more complicated than two objects, one of which is animated.  If your importer/exporter malfunctions on your current project, I have doubts that it will properly support the intricacies of armatures.